Vlad/Igor-Excalibre
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I picked the Cu/phenyl bromide example presicely as it is not too far from the chemistry I have been doing (at least part of the time) as part of polymer synthesis for the last eleven years. (you can see my ugly homepage on http://www.ch.cam.ac.uk/CUCL/staff/scm.html ) While in some cases I can hope to predict what reaction products are, in many cases there are twenty or thirty products - most of which I can never work out what they are. Most of the products are not thermodynamic products, but kinetic oddities. Even when I can work out the structure, some times it is “how on earth did that get made?”. Chemistry still throws plenty of surprises.
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“Enzymes are proteins. Enzymes catalyze reactions and make other reactions possible by physically holding compounds together in such a way that they bond, when otherwise such bonding would not occur without the enzyme”.
Yes but enzymes are chemicals and do chemical reactions! We can make artificial enzymes from scratch without a protein in sight, There is nothing an enzyme can do that we cant mimic (though often many many times worse). All biology is just chemistry that moves and eats! (don’t tell my biology friends I said that)
- “Look up computational organic chemistry, andsome of the people in the field”
I have to tutor computational chemistry and am well aware of its limitations and strengths. As a post-doc I modelled inorganic speciation in high temperature (300 C) water. I also use state of the art quantum modelling programmes such as Jaguar and Gaussian, all the time (admittedly not for following reactions)
Given a very well defined small reaction intermediate and substrate it is often possible to get close to calculating the correct product. However, up to now, we usually do it the other way round. “we got product X, what must the transition state be like?”. This is because the difference in energy between getting product X or Y is small (say several kcal/mol), which is usually the same order of magnitude error in calculating the transition states.
ab initio methods can give very accurate results, but at the moment on small systems (say 3-10 atoms). Larger systems are much much slower to calculate. The other problem with these methods is that you have to decide where you want your molecules to react and assign an approximate reaction path befoe the calculation- in other words you have to know what the reaction is you are studying. If the reaction in reality decides to react back to front from your model then your computor aint going to tell you! (e.g isocyanides can react either on the nitrogen or the carbon atom. If you didn’t know this and only modelled the nitrogen reaction, no computational programme at the moment would ever think “hmmm lets turn the molecule around and try the carbon”)
- “That particular reaction and many other simple ones are taught in high school and college first year organic chemistry classes. There are thousands of known reactions that allow you to predict what will happen in a given system, even if the reactants have never been mixed before.”
The combustion of methane with oxygen is a very complicated one, with multiradical pathways, probably 5-10 reactive intermediates. The products are simple, the reaction horribly convoluted. I dont know anyone that could even confidently model that one as most of the rate parameters are not known. It is certainly possible to simplify the model down where one could make reasonable calculations, but change the conditions dramatically and even the most confident modeller would simply say “do the experiment, and let me know the results so I can modify my model”
I feel that you are being fooled by what appear simple reactions giving thermodynamic products. 95% of chemistry is not like that (thank god). Let me put it this way - if could predict what you suggest we could, we could sack 90% of the current chemists, and the Nobel prize commitee would deliver me the chemistry prize every year by post.
- “Ok, so there’s bugs that convert hydrocarbons into energy. But care to point out where in the paper it states that they convert them into sugars?”
hmmm if bugs need sugars (for a hundred different uses including recognition and structure) and acetylene is only carbon source they use (e.g. ICI was developing biopol where methane could be used as the only carbon source for their bugs) then acetylene goes to make sugars. I only used that paper as an example of a quick google find. I could could trawl through the scientific literature using our databases to find exactly what you want but I have better things to do
5.“No, dear, all science is based on observation. Theories and models only exist to fit observations into a larger whole.”
My point was that we should in principle be able go to non chemistry-based theories (quantum mechanics) to fully explain chemical reactions. One day (probably fifty years) some one can say what happens if A and B react, and a physicist or mathematician will be able to come up with the answer from scratch, without a chemist saying “in my experience it goes to C”.
“but if so, the answer would require dozens of steps. There’s such a thing as simply having the sense to see what the likely result of a chemical reaction is. Indeed, combustion wasn’t specified in the homework problem (presumably) but a quick glance at the chemicals in question reveals it to be the only meaningful result. And it won’t produce molecular oxygen and hydrogen.”
but combustion takes dozens of steps (CH4 + O2 = CH3 + O2H, CH3 + O2 = CH3O2 etc etc) Change the conditions (e.g oxygen starve) and the main product could be CO, or C etc. You “know” that burning thing gives off CO2, but that is from experience (e.g. prior knowledge). Someone without your sense/experience would not have a clue what it gives. That was the OP point/question. Put it another way, are you sure that CH4 + O2 gives CO2 and H2O at 2000K. Are CO2 and H2O the thermodynamic products at 2000K?